公开(公告)号：US20060142947A1

公开(公告)日：2006-06-29

申请号：US11019183

申请日：2004-12-23

申请人： Peter Robrish ,  Nicholas Sampas ,  Ian Hardcastle

发明人： Peter Robrish ,  Nicholas Sampas ,  Ian Hardcastle

IPC分类号： G06F19/00

CPC分类号： G01N21/77 ,  G01N21/8483

摘要： A method of reading an assay includes illuminating a substrate. The substrate includes a sensitive region. The method also includes detecting whether the substrate was exposed to an analyte of interest. The detecting includes using low resolution detection and a priori data about the sensitive region to determine whether a characteristic of a first portion of the illumination returned from the sensitive region differs from a characteristic of a second portion of the illumination returned from the substrate outside the sensitive region.

摘要翻译： 读取测定法的方法包括照射衬底。 基板包括敏感区域。 该方法还包括检测底物是否暴露于感兴趣的分析物。 检测包括使用低分辨率检测和关于敏感区域的先验数据来确定从敏感区域返回的照明的第一部分的特性是否与敏感区域外的从衬底返回的照明的第二部分的特性不同 地区。

公开(公告)号：US20070067110A1

公开(公告)日：2007-03-22

申请号：US11232817

申请日：2005-09-21

申请人： Charles Nelson ,  Nicholas Sampas ,  Bo Curry

发明人： Charles Nelson ,  Nicholas Sampas ,  Bo Curry

IPC分类号： G06F19/00

CPC分类号： C12Q1/6876 ,  C12Q2600/166 ,  G16B25/00 ,  G16B30/00

摘要： The invention relates to methods and systems for generating negative controls for arrays. In an embodiment, the invention includes a method for generating a negative control probe sequence for an array including randomly generating a plurality of candidate negative control probes, screening the candidate negative control probes for sequence similarity to biologically occurring sequences, and screening the candidate negative control probes for one or more of base composition properties, primary structural features, secondary structural features, or thermodynamic characteristics. In an embodiment, the invention includes an apparatus for generating a negative control sequence for an array. The apparatus including a memory store and a programmable circuit in electrical communication with the memory store, the programmable circuit programmed to randomly generate a plurality of candidate probe sequences, screen the candidate probe sequences for sequence similarity to biologically occurring sequences, and screen the candidate probe sequences for one or more of base composition properties, primary structural features, secondary structural features, or thermodynamic characteristics.

摘要翻译： 本发明涉及用于产生阵列的负控制的方法和系统。 在一个实施方案中，本发明包括用于产生阵列的阴性对照探针序列的方法，包括随机产生多个候选阴性对照探针，筛选候选阴性对照探针以获得与生物学发生序列的序列相似性，以及筛选候选阴性对照 基础组合物性质，初级结构特征，二级结构特征或热力学特性中的一种或多种的探针。 在一个实施例中，本发明包括用于产生阵列的负控制序列的装置。 所述装置包括存储器存储器和与存储器存储器电通信的可编程电路，所述可编程电路被编程为随机生成多个候选探针序列，将候选探针序列筛选为与生物学发生序列的序列相似性，并筛选候选探针 基础组合物性质，初级结构特征，二级结构特征或热力学特征中的一种或多种的序列。

公开(公告)号：US20060094022A1

公开(公告)日：2006-05-04

申请号：US10978273

申请日：2004-10-30

申请人： Nicholas Sampas ,  Michael Barrett

发明人： Nicholas Sampas ,  Michael Barrett

IPC分类号： C12Q1/68 ,  G06F19/00

CPC分类号： C12Q1/6837

摘要： The present invention provides a method of performing an array hybridization analysis of a sample, including performing a restriction digest reaction on the sample, hybridizing the digested sample to the array, and interrogating the array. The array includes probe sets that provide for a determination of the extent of the restriction digest performed on the sample. Arrays including the probe sets are also described.

摘要翻译： 本发明提供了对样品进行阵列杂交分析的方法，包括对样品进行限制性消化反应，将消化的样品与阵列杂交，并询问阵列。 该阵列包括提供对样品进行的限制性消化酶的程度的测定的探针组。 还描述了包括探针组的阵列。

公开(公告)号：US20050049797A1

公开(公告)日：2005-03-03

申请号：US10650139

申请日：2003-08-27

申请人： Srinka Ghosh ,  Nicholas Sampas

发明人： Srinka Ghosh ,  Nicholas Sampas

IPC分类号： C40B40/06 ,  G01N31/00 ,  G01N33/48 ,  G01N33/50 ,  G06F19/00 ,  G06T7/00

CPC分类号： G06K9/32 ,  B01J2219/00608 ,  B01J2219/00689 ,  B01J2219/00693 ,  B01J2219/00722 ,  C40B40/06 ,  G06K2209/07 ,  G06T7/73 ,  G06T2207/30072 ,  G16B25/00

摘要： A method and system for detecting block and zone misalignment of feature positions within a microarray-data set and for correcting feature positions for block or zone misalignment. In one embodiment of the present invention, displacement vectors representing the vector differences between observed positions of features and expected positions for the features of a microarray are calculated, based on an initially determined coordinate system. Features within a microarray data set are then partitioned with respect to the calculated vector displacements, so that features misaligned by a common rotation or translation are partitioned into a separate partition. A correction for each common misalignment can then be calculated and applied to the features of each partition.

摘要翻译： 一种用于检测微阵列数据集内的特征位置的块和区域未对准并用于校正块或区域未对准的特征位置的方法和系统。 在本发明的一个实施例中，基于初始确定的坐标系，计算表示特征的观察位置与微阵列特征的预期位置之间的向量差的位移矢量。 然后将微阵列数据集中的特征相对于计算出的向量位移进行划分，使得通过公共旋转或平移不对准的特征被分割成单独的分区。 然后可以计算每个共同的未对准的校正并将其应用于每个分区的特征。

公开(公告)号：US20060073488A1

公开(公告)日：2006-04-06

申请号：US10959258

申请日：2004-10-05

申请人： Nicholas Sampas ,  Robert Ach

发明人： Nicholas Sampas ,  Robert Ach

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6837 ,  C12Q2545/101 ,  C12Q2537/143

摘要： The present invention relates to methods for detecting, quantitating, or standardizing binding to a nucleic acid array, standard polynucleotides that can be used in such methods, compositions including the standard polynucleotides, and methods of making the standard polynucleotides. An aspect of the present invention relates to a complete exon transcript of a gene. The gene can be a gene expressed as multiple transcripts but encoding only transcripts lacking at least a portion of at least one exon. A complete exon transcript includes all of the known bases of every known exon for such a gene. An aspect of the present invention relates to a method of detecting binding to a nucleic acid array. The method can include contacting the nucleic acid array with a standard polynucleotide for a gene. The standard polynucleotide for a gene includes all of the known bases of every known exon for that gene. In an embodiment, the standard polynucleotide includes a complete exon transcript of the gene.

摘要翻译： 本发明涉及用于检测，定量或标准化与核酸阵列结合的方法，可用于此类方法的标准多核苷酸，包含标准多核苷酸的组合物和制备标准多核苷酸的方法。 本发明的一个方面涉及基因的完整外显子转录物。 该基因可以是以多个转录物表达的基因，但仅编码缺少至少一部分至少一个外显子的转录本。 完整的外显子转录本包括所有已知的这种基因的外显子的已知碱基。 本发明的一个方面涉及检测与核酸阵列结合的方法。 该方法可以包括使核酸阵列与基因的标准多核苷酸接触。 基因的标准多核苷酸包括该基因的每个已知外显子的所有已知碱基。 在一个实施方案中，标准多核苷酸包括该基因的完整外显子转录物。

公开(公告)号：US5585639A

公开(公告)日：1996-12-17

申请号：US508021

申请日：1995-07-27

申请人： Andreas Dorsel ,  Nicholas Sampas

发明人： Andreas Dorsel ,  Nicholas Sampas

IPC分类号： G01N21/64

CPC分类号： G01N21/6452 ,  B01J2219/00707

摘要： An optical scanning apparatus for scanning an array of sample regions carried on the surface of a substrate is disclosed. The apparatus includes a beam generator for generating a light beam effective to produce detectable light from such sample regions, and scanning optics for scanning the beam in one direction corresponding to a linear array of such sample regions. Light emitted from the linear array is imaged through an imaging system whose optical axis is angularly offset from the optical axis of the illumination beam, onto a photodetector. The optical configuration achieves high performance with relatively simple optics.

摘要翻译： 公开了一种用于扫描载体在衬底表面上的样品区域阵列的光学扫描装置。 该装置包括用于产生有效产生来自这些样品区域的可检测光的光束的光束发生器，以及扫描光学元件，用于沿对应于这种样品区域的线性阵列的一个方向扫描光束。 从线性阵列发射的光通过成像系统成像，该成像系统的光轴与照明光束的光轴成角度地偏移到光电检测器上。 光学配置通过相对简单的光学器件实现高性能。

公开(公告)号：US20070128611A1

公开(公告)日：2007-06-07

申请号：US11292588

申请日：2005-12-02

申请人： Charles Nelson ,  Bo Curry ,  Nicholas Sampas

发明人： Charles Nelson ,  Bo Curry ,  Nicholas Sampas

IPC分类号： C12Q1/68 ,  G06F19/00

CPC分类号： C12Q1/6876 ,  C12Q1/6813 ,  C12Q2600/166 ,  G16B25/00 ,  G16B30/00 ,  C12Q2545/101

摘要： In an embodiment, a method is included for generating a negative control probe sequence for an array including selecting biological probe sequences from the array randomly, generating a plurality of candidate probe sequences by randomly permuting the selected biological probe sequence, and screening the candidate probe sequences for sequence similarity to biologically occurring sequences. An embodiment also includes a computer-readable medium having computer-executable instructions for performing a method for generating a negative control probe sequences. Embodiments can also include an apparatus for generating a negative control sequence for an array, as well as negative control probes, sets of negative control probes and arrays comprising at least one negative control probe.

摘要翻译： 在一个实施方案中，包括用于产生用于阵列的阴性对照探针序列的方法，包括随机选择阵列中的生物探针序列，通过随机置换所选生物探针序列产生多个候选探针序列，并筛选候选探针序列 与生物发生序列的序列相似性。 实施例还包括具有用于执行生成负控制探针序列的方法的计算机可执行指令的计算机可读介质。 实施例还可以包括用于产生阵列的负控制序列的装置，以及阴性对照探针，负控制探针组和包括至少一个阴性对照探针的阵列。

公开(公告)号：US20070059760A1

公开(公告)日：2007-03-15

申请号：US11599523

申请日：2006-11-13

申请人： Andreas Dorsel ,  David King ,  Nicholas Sampas

发明人： Andreas Dorsel ,  David King ,  Nicholas Sampas

IPC分类号： C12Q1/68 ,  C12M1/34

CPC分类号： G01N21/6452 ,  G01N21/6428

摘要： A method and apparatus of interrogating an addressable array unit, which includes a substrate, a light reflecting layer on a front side of the substrate, and a plurality of features on a front side of the array. The method may include, for each of multiple features, illuminating the feature simultaneously with reflected and non-reflected interrogating light. A light emitted from respective features is detected. Either or both, constructive interference of interrogating light at the features, or constructive interference of light emitted from the features, can be obtained to allow lowering of light power from the source, enhanced signal, or reduced noise, or combinations of the foregoing. High depth discrimination may also be obtained without the need for a confocal detection system with conventional pinhole.

摘要翻译： 一种询问可寻址阵列单元的方法和装置，其包括基板，在基板的前侧上的光反射层，以及阵列的前侧上的多个特征。 对于多个特征中的每一个，该方法可以包括与反射和未反射的询问光同时照亮特征。 检测从各个特征发射的光。 可以获得在特征中询问光的建构性干扰或从特征发射的光的建构性干扰，以允许降低源的光功率，增强的信号或降低的噪声或前述的组合。 也可以获得高深度鉴别，而不需要具有常规针孔的共焦检测系统。

公开(公告)号：US20060004527A1

公开(公告)日：2006-01-05

申请号：US10884731

申请日：2004-07-01

申请人： Nicholas Sampas ,  Jayati Ghosh

发明人： Nicholas Sampas ,  Jayati Ghosh

IPC分类号： C12Q1/68 ,  G06F19/00 ,  G01N33/48

CPC分类号： C12Q1/6837 ,  G16B25/00 ,  C12Q2545/101

摘要： Methods, systems and computer readable media for identifying dye-normalization probes. Intensity signals read from probes on a set of existing multi-channel microarrays are provided. The intensity signals are combined from each channel for each probe to generate a combined signal intensity value for each probe on each array. For each probe, the combined signal intensity values are combined across all arrays to provide an ordered sequence of probes from a lowest overall signal to a highest overall signal. The probes are then ranked according to the results of combining the combined signal intensity values, and binned into a plurality of bins. With regard to each probe, a metric representative of the multi-array distance of the signal intensities of the probe from a neutral expression value across all arrays is calculated and the probes are ranked within each bin based on the calculated metrics. Candidate dye-normalization probes may be selected by selecting at least one of the lowest ranked probes within each bin. Optionally, at least one of the lowest ranked probes in each bin may be discarded as outliers, and then at least one of the remaining lowest ranked probes may be selected from each bin as the candidate dye-normalization probes.

摘要翻译： 用于识别染料标准化探针的方法，系统和计算机可读介质。 提供了从一组现有的多通道微阵列上的探针读取的强度信号。 强度信号从每个探针的每个通道组合，以产生每个阵列上每个探针的组合信号强度值。 对于每个探针，将组合的信号强度值组合在所有阵列上，以从最低总信号到最高总信号提供探测器的有序序列。 然后根据组合信号强度值的结果对探针进行排序，并将其合并到多个箱中。 对于每个探针，计算表示探针的信号强度与所有阵列上的中性表达值的多阵列距离的度量，并且基于所计算的度量将探针排列在每个bin内。 可以通过选择每个箱中的至少一个最低排名的探针来选择候选染料标准化探针。 任选地，每个仓中最低排名的探针中的至少一个可以作为异常值被丢弃，然后可以从每个仓中选择剩余的最低排名的探针中的至少一个作为候选染料标准化探针。

公开(公告)号：US20050095595A1

公开(公告)日：2005-05-05

申请号：US10696177

申请日：2003-10-29

申请人： Richard Pittaro ,  Douglas Amorese ,  Carol Schembri ,  Leslie Leonard ,  Nicholas Sampas ,  Michael Caren

发明人： Richard Pittaro ,  Douglas Amorese ,  Carol Schembri ,  Leslie Leonard ,  Nicholas Sampas ,  Michael Caren

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6837 ,  C12Q2545/101

摘要： Systems and methods for optimizing polymer analysis are provided. One such system includes a polymer analysis system having a polymer control system. The polymer analysis system is operative to: apply a set of conditions to a sample being analyzed by the polymer array, the set of conditions correspond to at least one characteristic of the polymer array; analyze the at least one characteristic using the polymer control system; and generate polymer array data.

摘要翻译： 提供了优化聚合物分析的系统和方法。 一种这样的系统包括具有聚合物控制系统的聚合物分析系统。 聚合物分析系统可操作以：将一组条件应用于由聚合物阵列分析的样品，该组条件对应于聚合物阵列的至少一个特性; 使用聚合物控制系统分析至少一个特征; 并生成聚合物阵列数据。